Stamp, the metering tells you what a correct exposure (for the metering mode you have set) would be under the light that is currently reaching the camera. With that in mind, it does not incorporate the probable shooting of the flash into the reading, but the camera is aware that there is a flash and that it is set to fire.
So... if you have selected Av, it will try to expose the picture without taking into account the flash (from around 30segs to 1/250th or 1/200th), or you may tell it to use only 1/60th~1/250th, or to have the shutter fixed at 1/250th.
In Manual mode, you set the exposure (the metering assumes you won't be shooting flash for means of setting where the needle points) and, when taking the picture, the cam will instruct the flash how much power to use in order to have a correctly exposed image, with the settings you have selected (so it takes into account ISO and f). You can set the flash (depending on the model) to manual, and you have control over the amount of flash to fire, or, alternatively, you can set Flash Exposure Compensation in the camera to either reduce or increase the amount of light flashed.
Different modes (both on camera and on flash) are best suited for different situations and may be what you are after or not (also, each photographer will prefer certain methods over others). In Manual Mode, for both the camera and the flash, you have the highest degree of control, but it takes some practice to achieve good exposures. On the other hand, in Manual camera, Av, Tv, or P, the flash will try its best at exposing your image correctly (and in most modes of the preset area as well).
So, what I take it is you just need to adjust to a different information being displayed on the metering rather than anything else... the cam will behave as you expect it to, its just the metering information to the photographer that is different.
Rafa.